Weren't you concerned that the names in the annotation were incorrect?
You get to pick the names and the colors to be whatever you want to be.
By default, it uses FreeSurferColorLUT.txt.
doug
On 6/23/12 9:54 PM, Arno Klein wrote:
dear doug,
thank you for your response. for the custom color table, what do i
assign for the different anatomical names and color values? why
wouldn't the names and colors in FreeSurferColorLUT.txt work?
cheers,
@rno
Re: [Freesurfer] mris_label2annot mislabeling
Douglas N Greve
Wed, 20 Jun 2012 08:58:50 -0700
Arno, you need to create a custom color table (--ctab).
doug
On 06/20/2012 12:05 AM, Arno Klein wrote:
>
> hello!
>
> i have saved a couple of .label files and am trying to convert them to
> a .annot file with:
>
> mris_label2annot --h lh --s MMRR-21-1
> --l lh.superiorfrontal.label
> --l lh.superiorparietal.label
> --ctab FreeSurferColorLUT.txt --a output
>
> the stdout is:
>
> ColorTable atlas_colortable.txt
> AnnotName output
> nlables 2
> LabelThresh 0 0.000000
> Loading /usr/local/freesurfer/subjects/MMRR-21-1/surf/lh.orig
> 1 11829830 Left-Cerebral-Exterior
> 2 16119285 Left-Cerebral-White-Matter
> Mapping unhit to unknown
> ...
>
> clearly the anatomical names assigned are incorrect, and when i view
> the output with tksurfer, the labeled patches are in the right places
> but are assigned these same incorrect anatomical names.
>
> i have tried renaming the .label files to no avail. what am i doing
> wrong?
>
> cheers,
> @rno
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